Sodium in PDB 5tde: Tev Cleaved Human Atp Citrate Lyase Bound to Citrate

All present enzymatic activity of Tev Cleaved Human Atp Citrate Lyase Bound to Citrate:
2.3.3.8;

The structure of Tev Cleaved Human Atp Citrate Lyase Bound to Citrate, PDB code: 5tde was solved by J.Hu, M.E.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.39 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.828, 84.084, 194.781, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 18.4

The binding sites of Sodium atom in the Tev Cleaved Human Atp Citrate Lyase Bound to Citrate (pdb code 5tde). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Tev Cleaved Human Atp Citrate Lyase Bound to Citrate, PDB code: 5tde:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Tev Cleaved Human Atp Citrate Lyase Bound to Citrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Tev Cleaved Human Atp Citrate Lyase Bound to Citrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:23.6 occ:1.00 O B:HOH1202 2.1 35.3 1.0 O A:HOH771 2.3 34.1 1.0 OG1 A:FLC501 2.4 18.2 1.0 O1 B:2HP901 2.4 18.7 1.0 OG A:SER308 2.4 17.8 1.0 O A:HOH620 2.4 30.1 1.0 HB2 A:SER308 3.0 22.0 1.0 CB A:SER308 3.2 18.4 1.0 CGC A:FLC501 3.4 24.1 1.0 H A:GLY282 3.5 19.1 1.0 P B:2HP901 3.6 14.2 1.0 HB3 A:SER308 3.7 22.0 1.0 OG2 A:FLC501 3.8 25.2 1.0 HB3 A:SER263 3.8 30.2 1.0 O4 B:2HP901 3.9 20.0 1.0 HA2 A:GLY281 4.0 17.6 1.0 O2 B:2HP901 4.1 17.9 1.0 HA1 A:FLC501 4.2 15.9 1.0 HB2 A:SER263 4.2 30.2 1.0 HG A:SER263 4.2 33.7 1.0 OE1 A:GLU306 4.3 18.6 1.0 OE2 A:GLU306 4.4 27.5 1.0 N A:GLY282 4.4 15.9 1.0 CB A:SER263 4.4 25.2 1.0 H A:GLY309 4.5 18.3 1.0 CA A:SER308 4.5 16.1 1.0 O B:HOH1175 4.6 33.9 1.0 HOB A:FLC501 4.6 22.0 1.0 N A:GLY309 4.6 15.2 1.0 C A:SER308 4.7 16.9 1.0 CG A:FLC501 4.7 17.3 1.0 CD A:GLU306 4.7 19.5 1.0 O B:HOH1265 4.8 32.5 1.0 OG A:SER263 4.8 28.1 1.0 O B:HOH1309 4.8 28.6 1.0 HE2 B:HIS760 4.9 19.9 1.0 HA3 A:GLY282 4.9 16.6 1.0 CA A:GLY281 4.9 14.6 1.0 O3 B:2HP901 4.9 14.4 1.0 HG2 A:FLC501 4.9 20.8 1.0

Sodium binding site 2 out of 2 in the Tev Cleaved Human Atp Citrate Lyase Bound to Citrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Tev Cleaved Human Atp Citrate Lyase Bound to Citrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:31.5 occ:1.00 O A:ASP257 2.3 26.9 1.0 O A:SER260 2.3 30.8 1.0 O A:ALA262 2.3 21.5 1.0 O A:HOH917 2.4 34.3 1.0 OD1 A:ASP257 2.8 21.7 1.0 HA A:ASP257 3.2 30.3 1.0 C A:ASP257 3.3 29.2 1.0 C A:SER260 3.4 26.9 1.0 HA A:SER263 3.4 26.0 1.0 C A:ALA262 3.4 21.2 1.0 H A:SER260 3.5 44.3 1.0 CG A:ASP257 3.5 28.9 1.0 CA A:ASP257 3.7 25.3 1.0 HB3 A:SER260 3.9 44.0 1.0 C A:GLY261 4.0 25.3 1.0 O A:GLY261 4.1 29.7 1.0 N A:ALA262 4.2 23.5 1.0 HA2 A:GLY261 4.2 34.6 1.0 N A:SER260 4.2 37.0 1.0 CA A:SER260 4.2 34.9 1.0 CB A:ASP257 4.2 23.5 1.0 CA A:SER263 4.2 21.7 1.0 N A:SER263 4.2 19.5 1.0 OD2 A:ASP257 4.3 33.2 1.0 H A:LEU264 4.3 20.9 1.0 N A:GLY261 4.3 31.3 1.0 CA A:GLY261 4.4 28.8 1.0 CA A:ALA262 4.4 22.1 1.0 N A:ALA258 4.5 30.2 1.0 H A:ALA262 4.5 28.2 1.0 CB A:SER260 4.5 36.6 1.0 HA A:ALA258 4.6 41.5 1.0 HB3 A:ASP257 4.8 28.2 1.0 HZ2 A:LYS265 4.8 43.2 1.0 N A:LEU264 4.9 17.4 1.0 O A:LEU256 4.9 31.3 1.0 CA A:ALA258 4.9 34.6 1.0 HB2 A:ASP257 4.9 28.2 1.0

J.Hu, A.Komakula, M.E.Fraser. Binding of Hydroxycitrate to Human Atp-Citrate Lyase. Acta Crystallogr D Struct V. 73 660 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28777081
DOI: 10.1107/S2059798317009871